Baseline human gut microbiota profile in healthy people and standard reporting template

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

(2018) Guillaume Bernard et al.   Genome Biology and Evolution

Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

(2018) Dachao Liang et al.   Gut Pathogens

ReprDB and panDB: minimalist databases with maximal microbial representation

(2018) Wei Zhou et al.   Microbiome

Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits

(2017) Haiying Wang et al.   METHODS

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

(2017) Daniel E. Almonacid et al.   PLoS One

The gut microbiome of healthy Japanese and its microbial and functional uniqueness

(2016) Suguru Nishijima et al.   DNA RESEARCH

The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease

(2016) David N. O’Dwyer et al.   JOURNAL OF IMMUNOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

(2016) Vahan Simonyan et al.   Database-The Journal of Biological Databases and Curation

An assessment of US microbiome research

(2016) Elizabeth Stulberg et al.   Nature Microbiology

Helicobacter Pylori: A Nobel Pursuit?

(2016) Barry Marshall et al.   CANADIAN JOURNAL OF GASTROENTEROLOGY

Differences in Gut Microbiota Between Atopic and Healthy Children

(2015) Tiina Drell et al.   CURRENT MICROBIOLOGY

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology

(2015) Maria Carlota Dao et al.   GUT

Gut/brain axis and the microbiota

(2015) Emeran A. Mayer et al.   JOURNAL OF CLINICAL INVESTIGATION

The NIH Big Data to Knowledge (BD2K) initiative

(2015) P. E. Bourne et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

(2015) Adina Howe et al.   Frontiers in Microbiology

Remote homology and the functions of metagenomic dark matter

(2015) Briallen Lobb et al.   Frontiers in Genetics

Census-based rapid and accurate metagenome taxonomic profiling

(2014) Amirhossein Shamsaddini et al.   BMC GENOMICS

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

(2014) J. P. Zackular et al.   Cancer Prevention Research

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis

(2014) Luis Santana-Quintero et al.   PLoS One

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis

(2014) Vahan Simonyan et al.   Genes

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Virtual metagenome reconstruction from 16S rRNA gene sequences

(2012) Shujiro Okuda et al.   Nature Communications

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

The Human Microbiome Project in 2011 and Beyond

(2011) Lita M. Proctor   Cell Host & Microbe

Commensal Bacteroides Species Induce Colitis in Host-Genotype-Specific Fashion in a Mouse Model of Inflammatory Bowel Disease

(2011) Seth M. Bloom et al.   Cell Host & Microbe

Invasive potential of gut mucosa-derived fusobacterium nucleatum positively correlates with IBD status of the host

(2011) Jaclyn Strauss et al.   INFLAMMATORY BOWEL DISEASES

Oxidative stress-related responses of Bifidobacterium longum subsp. longum BBMN68 at the proteomic level after exposure to oxygen

(2011) M. Xiao et al.   MICROBIOLOGY-SGM

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

(2011) Chuming Chen et al.   PLoS One

Complete Genome Sequence of Bifidobacterium longum subsp. longum BBMN68, a New Strain from a Healthy Chinese Centenarian

(2010) Y. Hao et al.   JOURNAL OF BACTERIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

(2010) Sylvie Miquel et al.   PLoS One

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE